Certain chemicals tend to concentrate ("bioaccumulate") in fish to levels thousands of times greater than the levels in the water itself. The resulting concentrations in fish and the attendant health risks to those individuals who consume the fish, such as recreational and subsistence anglers, are of concern to government agencies and the public.

While the commission and its state partners are working to reduce the concentrations of toxic pollutants that bioaccumulate, basin states issue "advisories" containing meal advice for consumers of recreationally-caught fish and shellfish to minimize the risk to human health. These advisories list the water bodies, fish species, and number of meals recommended to minimize the risk. In some cases, no consumption of any fish species from a water body or more stringent consumption guidelines for pregnant women and children is advised. These advisories are typically revised yearly based upon recent fish tissue concentration data.

The commission does not issue its own fish consumption advisories. Rather, the commission works with its states and provides additional data for them to use to develop their state-issued advisories.